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It's weird because I've been doing the exact same thing for the last 10 days uploading as .xlsx and every time before today it worked fine and downloaded it as a .xlsx - the only changes I made were not excel-related but forum related with the permissioning to try to allow people to subscribe to read only topics so I thought it would be something to do with that - nothing else has changed on the site so I'm really confused as to why this would suddenly go wrong as I've tested in IE and Chrome. Maybe I will try just uploading it in a .zip file but it's one extra step in the process...grrr..why can s/w just not play nicely together !

The bottom line I think you will find is it up to the receiving program (in this case Excel) to identify the file extension and file type. Nothing else gets involved.

It still doesn't explain though why it identified it as .xlsx last 10 days until today - Guess I go down the zip route.

Mr Papa said
its a good question... and of course we dont alter the extension or file contents...  is it happening for all .xlsx files or just the one?   I have uploaded and read no less than six testing it out on multiple sites...

It's doing it for all of them, very confusing.

After much playing I found the culprit was a rewrite rule checkbox on the W3 Total Cache Plugin under the Miscellaneous setting which may be something to bear in mind if anyone else raises a similar query.